I’m willing to bet that these two files contain a different set of names (SAN):
/etc/letsencrypt/live/example.com/fullchain.pem
/etc/letsencrypt/live/example.com-0002/fullchain.pem
I’m willing to bet that these two files contain a different set of names (SAN):
/etc/letsencrypt/live/example.com/fullchain.pem
/etc/letsencrypt/live/example.com-0002/fullchain.pem